The advent of next-generation sequencing technologies is allowing researchers to perform studies and make discoveries which previously were not economically or technically feasible. Thus far, however, higher-throughput next-generation sequencing systems are relatively expensive, have relatively long run times and produce relatively short reads thereby limiting their use for diagnostic applications. In this Phase II application, we propose to combine the novel chip fabrication techniques developed in Phase I, the innovative sequencing by synthesis chemistry exclusively licensed from Columbia University, and an automated prototype sequencing instrument to produce an advanced sequencing by synthesis system. This system will be higher throughput and significantly more cost effective than other competing next-generation technologies. During the project, high density chips will be fabricated, the sequencing instrument and chemistry will be optimized and an E. coli genome will be re-sequenced. This system will be capable of producing large amounts of quality sequence data faster and at a lower cost than any other near-term next generation sequencing system. This will make next-generation DNA sequencing technology more accessible to the broad research community. PUBLIC HEALTH RELEVANCE: Ultimately, the ability to produce very inexpensive detailed DNA sequence information for complex organisms'genomes will both lead to accelerated discoveries throughout biology and provide the basis for Pharmacogenomics, a new paradigm in therapeutics wherein medicines are prescribed based on individual genotypes rather than just observed symptoms.